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EURASIP Journal on Bioinformatics and Systems Biology

ISSN: 1687--4145
Publisher: Hindawi Publishing Corporation


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Selection of Statistical Thresholds in Graphical Models

Author(s): Almudevar Anthony
Volume: 2009
Issue: 1
Year: 2009
Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints

Author(s): Yoon Byung-Jun
Volume: 2009
Issue: 1
Year: 2009
Stochastic Simulation of Delay-Induced Circadian Rhythms in Drosophila

Author(s): Xu Zhouyi | Cai Xiaodong
Volume: 2009
Issue: 1
Year: 2009
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks

Author(s): Hayashida Morihiro | Tamura Takeyuki | Akutsu Tatsuya | Zhang Shu-Qin | Ching Wai-Ki
Volume: 2008
Issue: 1
Year: 2008
A Time-Series-Based Feature Extraction Approach for Prediction of Protein Structural Class

Author(s): Gupta Ravi | Mittal Ankush | Singh Kuldip
Volume: 2008
Issue: 1
Year: 2008
Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

Author(s): Zhao Wentao | Agyepong Kwadwo | Serpedin Erchin | Dougherty Edward
Volume: 2008
Issue: 1
Year: 2008
Optimal Constrained Stationary Intervention in Gene Regulatory Networks

Author(s): Faryabi Babak | Vahedi Golnaz | Chamberland Jean-Francois | Datta Aniruddha | Dougherty Edward
Volume: 2008
Issue: 1
Year: 2008
Which Is Better: Holdout or Full-Sample Classifier Design?

Author(s): Brun Marcel | Xu Qian | Dougherty Edward
Volume: 2008
Issue: 1
Year: 2008
Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation

Author(s): Witt Johannes | Barisic Sandra | Sawodny Oliver | Ederer Michael | Kulms Dagmar | Sauter Thomas
Volume: 2011
Issue: 1
Year: 2011
Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks

Author(s): Koh Chushin | Wu Fang-Xiang | Selvaraj Gopalan | Kusalik Anthony
Volume: 2009
Issue: 1
Year: 2009
On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information

Author(s): Olsen Catharina | Meyer Patrick E | Bontempi Gianluca
Volume: 2009
Issue: 1
Year: 2009
Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length

Author(s): Dougherty John | Tabus Ioan | Astola Jaakko
Volume: 2008
Issue: 1
Year: 2008
Using Temporal Correlation in Factor Analysis for Reconstructing Transcription Factor Activities

Author(s): Pournara Iosifina | Wernisch Lorenz
Volume: 2008
Issue: 1
Year: 2008
Fixed Points in Discrete Models for Regulatory Genetic Networks

Author(s): Bollman Dorothy | Colón-Reyes Omar | Orozco Edusmildo
Volume: 2007
Issue: 1
Year: 2007
NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks

Author(s): Kontkanen Petri | Wettig Hannes | Myllymäki Petri
Volume: 2007
Issue: 1
Year: 2007
A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification

Author(s): Hemmerich Chris | Kim Sun
Volume: 2007
Issue: 1
Year: 2007
Comparison of Gene Regulatory Networks via Steady-State Trajectories

Author(s): Brun Marcel | Kim Seungchan | Choi Woonjung | Dougherty Edward
Volume: 2007
Issue: 1
Year: 2007
Information-Theoretic Inference of Large Transcriptional Regulatory Networks

Author(s): Meyer Patrick | Kontos Kevin | Lafitte Frederic | Bontempi Gianluca
Volume: 2007
Issue: 1
Year: 2007
Information Theoretic Methods for Bioinformatics

Author(s): Rissanen Jorma | Grünwald Peter | Heikkonen Jukka | Myllymäki Petri | Roos Teemu | Rousu Juho
Volume: 2007
Issue: 1
Year: 2007
A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

Author(s): Trepode Nestor | Armelin Hugo | Bittner Michael | Barrera Junior | Gubitoso Marco | Hashimoto Ronaldo
Volume: 2007
Issue: 1
Year: 2007
Aligning Sequences by Minimum Description Length

Author(s): Conery JohnS
Volume: 2007
Issue: 1
Year: 2007
Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization

Author(s): Luna Isabel | Huang Yufei | Yin Yufang | Padillo Diego | Perez M Carmen
Volume: 2007
Issue: 1
Year: 2007
Clustering Time-Series Gene Expression Data Using Smoothing Spline Derivatives

Author(s): Déjean S | Martin PGP | Baccini A | Besse P
Volume: 2007
Issue: 1
Year: 2007
Gene Selection for Multiclass Prediction by Weighted Fisher Criterion

Author(s): Xuan Jianhua | Wang Yue | Dong Yibin | Feng Yuanjian | Wang Bin | Khan Javed | Bakay Maria | Wang Zuyi | Pachman Lauren | Winokur Sara | Chen Yi-Wen | Clarke Robert | Hoffman Eric
Volume: 2007
Issue: 1
Year: 2007
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

Author(s): Suzuki Haruo | Saito Rintaro | Tomita Masaru
Volume: 2007
Issue: 1
Year: 2007
Compressing Proteomes: The Relevance of Medium Range Correlations

Author(s): Benedetto Dario | Caglioti Emanuele | Chica Claudia
Volume: 2007
Issue: 1
Year: 2007
Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

Author(s): Jose Hena | Vadivukarasi Thangavel | Devakumar Jyothi
Volume: 2007
Issue: 1
Year: 2007
Inferring Time-Varying Network Topologies from Gene Expression Data

Author(s): Rao Arvind | Hero Alfred | States David | Engel James
Volume: 2007
Issue: 1
Year: 2007
Analysis of Gene Coexpression by B-Spline Based CoD Estimation

Author(s): Li Huai | Sun Yu | Zhan Ming
Volume: 2007
Issue: 1
Year: 2007
Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model

Author(s): Aburatani Sachiyo | Sun Fuyan | Saito Shigeru | Honda Masao | Kaneko Shu-ichi | Horimoto Katsuhisa
Volume: 2007
Issue: 1
Year: 2007
Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells

Author(s): Niemistö Antti | Nykter Matti | Aho Tommi | Jalovaara Henna | Marjanen Kalle | Ahdesmäki Miika | Ruusuvuori Pekka | Tiainen Mikko | Linne Marja-Leena | Yli-Harja Olli
Volume: 2007
Issue: 1
Year: 2007
A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

Author(s): Gupta Ravi | Sarthi Divya | Mittal Ankush | Singh Kuldip
Volume: 2007
Issue: 1
Year: 2007
The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

Author(s): Song JZ | Duan KM | Ware T | Surette M
Volume: 2007
Issue: 1
Year: 2007
Decorrelation of the True and Estimated Classifier Errors in High-Dimensional Settings

Author(s): Hanczar Blaise | Hua Jianping | Dougherty Edward
Volume: 2007
Issue: 1
Year: 2007
The -Version of the Cramér-von Mises Test for Two-Sample Comparisons in Microarray Data Analysis

Author(s): Xiao Yuanhui | Gordon Alexander | Yakovlev Andrei
Volume: 2006
Issue: 1
Year: 2006
Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics

Author(s): Georgiev Nikola | Petrov Valko | Georgiev Georgi
Volume: 2006
Issue: 1
Year: 2006
Normalization Benefits Microarray-Based Classification

Author(s): Hua Jianping | Balagurunathan Yoganand | Chen Yidong | Lowey James | Bittner Michael | Xiong Zixiang | Suh Edward | Dougherty Edward
Volume: 2006
Issue: 1
Year: 2006
Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Author(s): Chiu David | Wang Yan
Volume: 2006
Issue: 1
Year: 2006
Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

Author(s): Ponnala Lalit | Stomp Anne-Marie | Bitzer Donald | Vouk Mladen
Volume: 2006
Issue: 1
Year: 2006
A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana

Author(s): Henkel Sebastian | Nägele Thomas | Hörmiller Imke | Sauter Thomas | Sawodny Oliver | Ederer Michael | Heyer Arnd
Volume: 2011
Issue: 1
Year: 2011
Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks

Author(s): Dimitrova Elena | Mitra Indranil | Jarrah Abdul
Volume: 2011
Issue: 1
Year: 2011
A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data

Author(s): Epps Julien
Volume: 2009
Issue: 1
Year: 2009
How to Improve Postgenomic Knowledge Discovery Using Imputation

Author(s): Sehgal Muhammad Shoaib B | Gondal Iqbal | Dooley Laurence S | Coppel Ross
Volume: 2009
Issue: 1
Year: 2009
Network Structure and Biological Function: Reconstruction, Modeling, and Statistical Approaches

Author(s): Selbig Joachim | Steinfath Matthias | Repsilber Dirk
Volume: 2009
Issue: 1
Year: 2009
Spectral Preprocessing for Clustering Time-Series Gene Expressions

Author(s): Zhao Wentao | Serpedin Erchin | Dougherty Edward R
Volume: 2009
Issue: 1
Year: 2009
Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge

Author(s): Zhao Wentao | Serpedin Erchin | Dougherty Edward R
Volume: 2009
Issue: 1
Year: 2009
Reverse Engineering of Gene Regulatory Networks: A Comparative Study

Author(s): Hache Hendrik | Lehrach Hans | Herwig Ralf
Volume: 2009
Issue: 1
Year: 2009
Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

Author(s): Song Mingzhou(Joe) | Lewis Chris K | Lance Eric R | Chesler Elissa J | Yordanova Roumyana Kirova | Langston Michael A | Lodowski Kerrie H | Bergeson Susan E
Volume: 2009
Issue: 1
Year: 2009
Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data—A Model-Based Study

Author(s): Sun Youting | Braga-Neto Ulisses | Dougherty EdwardR
Volume: 2009
Issue: 1
Year: 2009
Origins of Stochasticity and Burstiness in High-Dimensional Biochemical Networks

Author(s): Rosenfeld Simon
Volume: 2009
Issue: 1
Year: 2009
Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited

Author(s): Faryabi Babak | Vahedi Golnaz | Chamberland Jean-Francois | Datta Aniruddha | Dougherty EdwardR
Volume: 2009
Issue: 1
Year: 2009
Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics

Author(s): Serpedin Erchin | Garcia-Frias Javier | Huang Yufei | Braga-Neto Ulisses
Volume: 2009
Issue: 1
Year: 2009
Clustering of Gene Expression Data Based on Shape Similarity

Author(s): Hestilow Travis J | Huang Yufei
Volume: 2009
Issue: 1
Year: 2009
Compressive Sensing DNA Microarrays

Author(s): Dai Wei | Sheikh Mona A | Milenkovic Olgica | Baraniuk Richard G
Volume: 2009
Issue: 1
Year: 2009
Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?

Author(s): Vu TT | Braga-Neto UM
Volume: 2009
Issue: 1
Year: 2009
Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

Author(s): Andorf Sandra | Gärtner Tanja | Steinfath Matthias | Witucka-Wall Hanna | Altmann Thomas | Repsilber Dirk
Volume: 2009
Issue: 1
Year: 2009
Inference of Boolean Networks Using Sensitivity Regularization

Author(s): Liu Wenbin | Lähdesmäki Harri | Dougherty Edward | Shmulevich Ilya
Volume: 2008
Issue: 1
Year: 2008
Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text

Author(s): Gaudan S | Jimeno Yepes A | Lee V | Rebholz-Schuhmann D
Volume: 2008
Issue: 1
Year: 2008
Integrating Biosystem Models Using Waveform Relaxation

Author(s): Li Linzhong | Seymour RobertM | Baigent Stephen
Volume: 2008
Issue: 1
Year: 2008
Gene Regulatory Network Reconstruction Using Conditional Mutual Information

Author(s): Liang Kuo-Ching | Wang Xiaodong
Volume: 2008
Issue: 1
Year: 2008
Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data

Author(s): Zhao Wentao | Serpedin Erchin | Dougherty Edward
Volume: 2008
Issue: 1
Year: 2008
Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

Author(s): Gupta Rashi | Arjas Elja | Kulathinal Sangita | Thomas Andrew | Auvinen Petri
Volume: 2008
Issue: 1
Year: 2008
Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence

Author(s): Marshall Stephen | Yu Le | Xiao Yufei | Dougherty Edward
Volume: 2007
Issue: 1
Year: 2007
Splitting the BLOSUM Score into Numbers of Biological Significance

Author(s): Fabris Francesco | Sgarro Andrea | Tossi Alessandro
Volume: 2007
Issue: 1
Year: 2007
Question Processing and Clustering in INDOC: A Biomedical Question Answering System

Author(s): Sondhi Parikshit | Raj Purushottam | Kumar V Vinod | Mittal Ankush
Volume: 2007
Issue: 1
Year: 2007
Algorithms for Finding Small Attractors in Boolean Networks

Author(s): Zhang Shu-Qin | Hayashida Morihiro | Akutsu Tatsuya | Ching Wai-Ki | Ng Michael
Volume: 2007
Issue: 1
Year: 2007
Genetic Regulatory Networks

Author(s): Dougherty Edward | Akutsu Tatsuya | Dan Cristea Paul | Tewfik Ahmed
Volume: 2007
Issue: 1
Year: 2007
Quantification of the Impact of Feature Selection on the Variance of Cross-Validation Error Estimation

Author(s): Xiao Yufei | Hua Jianping | Dougherty Edward
Volume: 2007
Issue: 1
Year: 2007
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

Author(s): Aktulga Hasan | Kontoyiannis Ioannis | Lyznik L Alex | Szpankowski Lukasz | Grama Ananth | Szpankowski Wojciech
Volume: 2007
Issue: 1
Year: 2007
Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

Author(s): Rao Arvind | Hero Alfred | States David | Engel James
Volume: 2007
Issue: 1
Year: 2007
Functional Classification of Genome-Scale Metabolic Networks

Author(s): Ebenhöh Oliver | Handorf Thomas
Volume: 2009
Issue: 1
Year: 2009
Transition Dependency: A Gene-Gene Interaction Measure for Times Series Microarray Data

Author(s): Gao Xin | Pu Daniel Q | Song Peter X-K
Volume: 2009
Issue: 1
Year: 2009
TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites

Author(s): Weir Michael P | Rice Michael D
Volume: 2010
Issue: 1
Year: 2010
A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process

Author(s): Chen Jie | Yiğiter Ayten | Wang Yu-Ping | Deng Hong-Wen
Volume: 2010
Issue: 1
Year: 2010
A Hypothesis Test for Equality of Bayesian Network Models

Author(s): Almudevar Anthony
Volume: 2010
Issue: 1
Year: 2010
Polynomial-Time Algorithm for Controllability Test of a Class of Boolean Biological Networks

Author(s): Kobayashi Koichi | Imura Jun-Ichi | Hiraishi Kunihiko
Volume: 2010
Issue: 1
Year: 2010
Progression Analysis and Stage Discovery in Continuous Physiological Processes Using Image Computing

Author(s): Shamir Lior | Rahimi Salim | Orlov Nikita | Ferrucci Luigi | Goldberg Ilya
Volume: 2010
Issue: 1
Year: 2010
Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models

Author(s): Manninen Tiina | Hituri Katri | Toivari Eeva | Linne Marja-Leena
Volume: 2011
Issue: 1
Year: 2011
Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D

Author(s): Aćimović J | Mäki-Marttunen T | Havela R | Teppola H | Linne M-L
Volume: 2011
Issue: 1
Year: 2011
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation

Author(s): Mannerstrom Henrik | Yli-Harja Olli | Ribeiro Andre
Volume: 2011
Issue: 1
Year: 2011
Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

Author(s): Baker Syed | Poskar C | Junker Björn
Volume: 2011
Issue: 1
Year: 2011
Measuring and analyzing tissue specificity of human genes and protein complexes

Author(s): Emig Dorothea | Kacprowski Tim | Albrecht Mario
Volume: 2011
Issue: 1
Year: 2011
Adaptive Dynamics of Regulatory Networks: Size Matters

Author(s): Repsilber Dirk | Martinetz Thomas | Björklund Mats
Volume: 2009
Issue: 1
Year: 2009
Assessing the Exceptionality of Coloured Motifs in Networks

Author(s): Schbath Sophie | Lacroix Vincent | Sagot Marie-France
Volume: 2009
Issue: 1
Year: 2009
A Bayesian Network View on Nested Effects Models

Author(s): Zeller Cordula | Fröhlich Holger | Tresch Achim
Volume: 2009
Issue: 1
Year: 2009
MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

Author(s): Evans Scott | Kourtidis Antonis | Markham T Stephen | Miller Jonathan | Conklin Douglas | Torres Andrew
Volume: 2007
Issue: 1
Year: 2007
IB, NF-B Regulation Model: Simulation Analysis of Small Number of Molecules

Author(s): Sarkar Anamika | Meila Marina | Franza Robert
Volume: 2007
Issue: 1
Year: 2007
Using Temporal Correlation in Factor Analysis for Reconstructing Transcription Factor Activities

Author(s): Iosifina Pournara | Lorenz Wernisch
Volume: 2008
Year: 2008
Inference of Boolean Networks Using Sensitivity Regularization

Author(s): Wenbin Liu | Harri Lähdesmäki | Edward R. Dougherty | Ilya Shmulevich
Volume: 2008
Year: 2008
Gene Regulatory Network Reconstruction Using Conditional Mutual Information

Author(s): Kuo-Ching Liang | Xiaodong Wang
Volume: 2008
Year: 2008
Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data

Author(s): Wentao Zhao | Erchin Serpedin | Edward R. Dougherty
Volume: 2008
Year: 2008
Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

Author(s): Arvind Rao | Alfred O. Hero III | David J. States | James Douglas Engel
Volume: 2007
Year: 2007
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

Author(s): Hasan Metin Aktulga | Ioannis Kontoyiannis | L. Alex Lyznik | Lukasz Szpankowski | Ananth Y. Grama | Wojciech Szpankowski
Volume: 2007
Year: 2007
MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

Author(s): Scott C. Evans | Antonis Kourtidis | T. Stephen Markham | Jonathan Miller | Douglas S. Conklin | Andrew S. Torres
Volume: 2007
Year: 2007
A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

Author(s): Nestor Walter Trepode | Hugo Aguirre Armelin | Michael Bittner | Junior Barrera | Marco Dimas Gubitoso | Ronaldo Fumio Hashimoto
Volume: 2007
Year: 2007
Comparison of Gene Regulatory Networks via Steady-State Trajectories

Author(s): Marcel Brun | Seungchan Kim | Woonjung Choi | Edward R. Dougherty
Volume: 2007
Year: 2007
Fixed Points in Discrete Models for Regulatory Genetic Networks

Author(s): Dorothy Bollman | Omar Colón-Reyes | Edusmildo Orozco
Volume: 2007
Year: 2007
Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence

Author(s): Stephen Marshall | Le Yu | Yufei Xiao | Edward R. Dougherty
Volume: 2007
Year: 2007
Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization

Author(s): Isabel Tienda Luna | Yufei Huang | Yufang Yin | Diego P. Ruiz Padillo | M. Carmen Carrion Perez
Volume: 2007
Year: 2007
Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model

Author(s): Sachiyo Aburatani | Fuyan Sun | Shigeru Saito | Masao Honda | Shu-ichi Kaneko | Katsuhisa Horimoto
Volume: 2007
Year: 2007
Analysis of Gene Coexpression by B-Spline Based CoD Estimation

Author(s): Huai Li | Yu Sun | Ming Zhan
Volume: 2007
Year: 2007
Decorrelation of the True and Estimated Classifier Errors in High-Dimensional Settings

Author(s): Blaise Hanczar | Jianping Hua | Edward R. Dougherty
Volume: 2007
Year: 2007
Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells

Author(s): Antti Niemistö | Matti Nykter | Tommi Aho | Henna Jalovaara | Kalle Marjanen | Miika Ahdesmäki | Pekka Ruusuvuori | Mikko Tiainen | Marja-Leena Linne | Olli Yli-Harja
Volume: 2007
Year: 2007
Gene Selection for Multiclass Prediction by Weighted Fisher Criterion

Author(s): Jianhua Xuan | Yue Wang | Yibin Dong | Yuanjian Feng | Bin Wang | Javed Khan | Maria Bakay | Zuyi Wang | Lauren Pachman | Sara Winokur | Yi-Wen Chen | Robert Clarke | Eric Hoffman
Volume: 2007
Year: 2007
Clustering Time-Series Gene Expression Data Using Smoothing Spline Derivatives

Author(s): S. Déjean | P. G. P. Martin | A. Baccini | P. Besse
Volume: 2007
Year: 2007
The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

Author(s): J. Z. Song | K. M. Duan | T. Ware | M. Surette
Volume: 2007
Year: 2007
A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

Author(s): Ravi Gupta | Divya Sarthi | Ankush Mittal | Kuldip Singh
Volume: 2007
Year: 2007
Quantification of the Impact of Feature Selection on the Variance of Cross-Validation Error Estimation

Author(s): Yufei Xiao | Jianping Hua | Edward R. Dougherty
Volume: 2007
Year: 2007
Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

Author(s): Lalit Ponnala | Anne-Marie Stomp | Donald L. Bitzer | Mladen A. Vouk
Volume: 2006
Year: 2006
Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics

Author(s): Nikola Georgiev | Valko Petrov | Georgi Georgiev
Volume: 2006
Year: 2006
The L1-Version of the Cramér-von Mises Test for Two-Sample Comparisons in Microarray Data Analysis

Author(s): Yuanhui Xiao | Alexander Gordon | Andrei Yakovlev
Volume: 2006
Year: 2006
Normalization Benefits Microarray-Based Classification

Author(s): Jianping Hua | Yoganand Balagurunathan | Yidong Chen | James Lowey | Michael L. Bittner | Zixiang Xiong | Edward Suh | Edward R. Dougherty
Volume: 2006
Year: 2006
Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Author(s): David K. Y. Chiu | Yan Wang
Volume: 2006
Year: 2006
Polynomial-Time Algorithm for Controllability Test of a Class of Boolean Biological Networks

Author(s): Koichi Kobayashi | Jun-Ichi Imura | Kunihiko Hiraishi
Volume: 2010
Year: 2010
Progression Analysis and Stage Discovery in Continuous Physiological Processes Using Image Computing

Author(s): Lior Shamir | Salim Rahimi | Nikita Orlov | Luigi Ferrucci | Ilya G. Goldberg
Volume: 2010
Year: 2010
Selection of Statistical Thresholds in Graphical Models

Author(s): Anthony Almudevar
Volume: 2009
Year: 2009
Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data—A Model-Based Study

Author(s): Youting Sun | Ulisses Braga-Neto | Edward R. Dougherty
Volume: 2009
Year: 2009
Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks

Author(s): Chushin Koh | Fang-Xiang Wu | Gopalan Selvaraj | Anthony J. Kusalik
Volume: 2009
Year: 2009
Stochastic Simulation of Delay-Induced Circadian Rhythms in Drosophila

Author(s): Zhouyi Xu | Xiaodong Cai
Volume: 2009
Year: 2009
Reverse Engineering of Gene Regulatory Networks: A Comparative Study

Author(s): Hendrik Hache | Hans Lehrach | Ralf Herwig
Volume: 2009
Year: 2009
Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited

Author(s): Babak Faryabi | Golnaz Vahedi | Jean-Francois Chamberland | Aniruddha Datta | Edward R. Dougherty
Volume: 2009
Year: 2009
Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?

Author(s): T. T. Vu | U. M. Braga-Neto
Volume: 2009
Year: 2009
Spectral Preprocessing for Clustering Time-Series Gene Expressions

Author(s): Wentao Zhao | Erchin Serpedin | Edward R. Dougherty
Volume: 2009
Year: 2009
Clustering of Gene Expression Data Based on Shape Similarity

Author(s): Travis J. Hestilow | Yufei Huang
Volume: 2009
Year: 2009
Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge

Author(s): Wentao Zhao | Erchin Serpedin | Edward R. Dougherty
Volume: 2009
Year: 2009
Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

Author(s): Mingzhou (Joe) Song | Chris K. Lewis | Eric R. Lance | Elissa J. Chesler | Roumyana Kirova Yordanova | Michael A. Langston | Kerrie H. Lodowski | Susan E. Bergeson
Volume: 2009
Year: 2009
Functional Classification of Genome-Scale Metabolic Networks

Author(s): Oliver Ebenhöh | Thomas Handorf
Volume: 2009
Year: 2009
Adaptive Dynamics of Regulatory Networks: Size Matters

Author(s): Dirk Repsilber | Thomas Martinetz | Mats Björklund
Volume: 2009
Year: 2009
How to Improve Postgenomic Knowledge Discovery Using Imputation

Author(s): Muhammad Shoaib B. Sehgal | Iqbal Gondal | Laurence S. Dooley | Ross Coppel
Volume: 2009
Year: 2009
Transition Dependency: A Gene-Gene Interaction Measure for Times Series Microarray Data

Author(s): Xin Gao | Daniel Q. Pu | Peter X.-K. Song
Volume: 2009
Year: 2009
Assessing the Exceptionality of Coloured Motifs in Networks

Author(s): Sophie Schbath | Vincent Lacroix | Marie-France Sagot
Volume: 2009
Year: 2009
Compressive Sensing DNA Microarrays

Author(s): Wei Dai | Mona A. Sheikh | Olgica Milenkovic | Richard G. Baraniuk
Volume: 2009
Year: 2009
On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information

Author(s): Catharina Olsen | Patrick E. Meyer | Gianluca Bontempi
Volume: 2009
Year: 2009
Integrating Biosystem Models Using Waveform Relaxation

Author(s): Linzhong Li | Robert M. Seymour | Stephen Baigent
Volume: 2008
Year: 2008
Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models

Author(s): Tiina Manninen | Katri Hituri | Eeva Toivari | Marja-Leena Linne
Volume: 2011
Year: 2011
Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D

Author(s): J. Aćimović | T. Mäki-Marttunen | R. Havela | H. Teppola | M.-L. Linne
Volume: 2011
Year: 2011
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation

Author(s): Henrik Mannerstrom | Olli Yli-Harja | Andre S. Ribeiro
Volume: 2011
Year: 2011
TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites

Author(s): Michael P. Weir | Michael D. Rice
Volume: 2010
Year: 2010
A Hypothesis Test for Equality of Bayesian Network Models

Author(s): Anthony Almudevar
Volume: 2010
Year: 2010
A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process

Author(s): Jie Chen | Ayten Yiğiter | Yu-Ping Wang | Hong-Wen Deng
Volume: 2010
Year: 2010
Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks

Author(s): P. van Nes | D. Bellomo | M. J. T. Reinders | D. de Ridder
Volume: 2009
Year: 2009
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks

Author(s): Morihiro Hayashida | Takeyuki Tamura | Tatsuya Akutsu | Shu-Qin Zhang | Wai-Ki Ching
Volume: 2008
Year: 2008
Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

Author(s): Sandra Andorf | Tanja Gärtner | Matthias Steinfath | Hanna Witucka-Wall | Thomas Altmann | Dirk Repsilber
Volume: 2009
Year: 2008
NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks

Author(s): Petri Kontkanen | Hannes Wettig | Petri Myllymäki
Volume: 2007
Year: 2008
Aligning Sequences by Minimum Description Length

Author(s): John S. Conery
Volume: 2007
Year: 2008
IκB, NF-κB Regulation Model: Simulation Analysis of Small Number of Molecules

Author(s): Anamika Sarkar | Marina Meila | Robert B. Franza
Volume: 2007
Year: 2008
Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

Author(s): Hena Jose | Thangavel Vadivukarasi | Jyothi Devakumar
Volume: 2007
Year: 2007
Question Processing and Clustering in INDOC: A Biomedical Question Answering System

Author(s): Parikshit Sondhi | Purushottam Raj | V. Vinod Kumar | Ankush Mittal
Volume: 2007
Year: 2007
Compressing Proteomes: The Relevance of Medium Range Correlations

Author(s): Dario Benedetto | Emanuele Caglioti | Claudia Chica
Volume: 2007
Year: 2007
Information-Theoretic Inference of Large Transcriptional Regulatory Networks

Author(s): Patrick E. Meyer | Kevin Kontos | Frederic Lafitte | Gianluca Bontempi
Volume: 2007
Year: 2007
Algorithms for Finding Small Attractors in Boolean Networks

Author(s): Shu-Qin Zhang | Morihiro Hayashida | Tatsuya Akutsu | Wai-Ki Ching | Michael K. Ng
Volume: 2007
Year: 2007
Inferring Time-Varying Network Topologies from Gene Expression Data

Author(s): Arvind Rao | Alfred O. Hero III | David J. States | James Douglas Engel
Volume: 2007
Year: 2007
Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

Author(s): Wentao Zhao | Kwadwo Agyepong | Erchin Serpedin | Edward R. Dougherty
Volume: 2008
Year: 2008
Optimal Constrained Stationary Intervention in Gene Regulatory Networks

Author(s): Babak Faryabi | Golnaz Vahedi | Jean-Francois Chamberland | Aniruddha Datta | Edward R. Dougherty
Volume: 2008
Year: 2008
A Time-Series-Based Feature Extraction Approach for Prediction of Protein Structural Class

Author(s): Ravi Gupta | Ankush Mittal | Kuldip Singh
Volume: 2008
Year: 2008
Which Is Better: Holdout or Full-Sample Classifier Design?

Author(s): Marcel Brun | Qian Xu | Edward R. Dougherty
Volume: 2008
Year: 2008
Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

Author(s): Rashi Gupta | Elja Arjas | Sangita Kulathinal | Andrew Thomas | Petri Auvinen
Volume: 2008
Year: 2008
Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text

Author(s): S. Gaudan | A. Jimeno Yepes | V. Lee | D. Rebholz-Schuhmann
Volume: 2008
Year: 2008
Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length

Author(s): John Dougherty | Ioan Tabus | Jaakko Astola
Volume: 2008
Year: 2008
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

Author(s): Haruo Suzuki | Rintaro Saito | Masaru Tomita
Volume: 2007
Year: 2007
Splitting the BLOSUM Score into Numbers of Biological Significance

Author(s): Francesco Fabris | Andrea Sgarro | Alessandro Tossi
Volume: 2007
Year: 2007
A Bayesian Network View on Nested Effects Models

Author(s): Cordula Zeller | Holger Fröhlich | Achim Tresch
Volume: 2009
Year: 2009
Network Structure and Biological Function: Reconstruction, Modeling, and Statistical Approaches

Author(s): Joachim Selbig | Matthias Steinfath | Dirk Repsilber
Volume: 2009
Year: 2009
Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics

Author(s): Erchin Serpedin | Javier Garcia-Frias | Yufei Huang | Ulisses Braga-Neto
Volume: 2009
Year: 2009
Information Theoretic Methods for Bioinformatics

Author(s): Jorma Rissanen | Peter Grünwald | Jukka Heikkonen | Petri Myllymäki | Teemu Roos | Juho Rousu
Volume: 2007
Year: 2008
Genetic Regulatory Networks

Author(s): Edward R. Dougherty | Tatsuya Akutsu | Paul Dan Cristea | Ahmed H. Tewfik
Volume: 2007
Year: 2007
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