Journal Articles

2016, submitted [118] Can genome-scale gene regulatory networks be experimentally validated? Differences between biological and clinical validations , In , volume , 2016, submitted. [117] Smoking and increased age in hematuria patients significantly confound the accuracy of classifiers for the diagnosis of urothelial cancer , In , volume , 2016, submitted. 2016, revised [116] A Review of Connectivity Mapping and Computational Approaches in Pharmacogenomics , In Briefings in Bioinformatics, volume , 2016, revised. 2016 [115] Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites , In Frontiers in Genetics, volume 7, 2016. [114] Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules , In BMC Bioinformatics, volume 17, 2016. [113] The Need for Formally Defining 'Modern Medicine' by Means of Experimental Design , In Frontiers in Genetics, volume 7, 2016. [112] samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files , In Bioinformatics, volume , 2016. [111] Fifty Years of Graph Matching, Network Alignment and Network Comparison , In Information Sciences, volume 346?347, 2016. [110] The process of analyzing data is the emergent feature of data science , In Frontiers in Genetics, volume 7, 2016. [109] A BRCA1 deficient, NF$\kappa$B driven immune signal predicts good outcome in Triple Negative breast cancer , In Oncotarget, volume 7, 2016. [108] Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline , In Briefings in Bioinformatics, volume 17, 2016. 2015, submitted [107] The evolution of modularity in protein networks: A second-order gene duplication model , In , 2015, submitted. 2015 [106] Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices , In PLoS ONE, Public Library of Science, volume 10, 2015. [105] Urinary Thrombomodulin Levels Were Significantly Higher Following Occupational Exposure to Chemicals, In The Presence of Dipstick Protein, But Not in the Presence of Dipstick Blood , In Biology and Medicine, volume 7, 2015. [104] Graph distance measures based on topological indices revisited , In Applied Mathematics and Computation, volume 266, 2015. () [103] Entropy of weighted graphs with Randi\'c weights , In Entropy, volume 17, 2015. [102] Using shRNA experiments to validate gene regulatory networks , In Genomics Data, volume 4, 2015. () [101] Biological networks: The microscope of the 21st century? , In Frontiers in Genetics, volume 6, 2015. [100] Effects of subsampling on characteristics of RNA-seq data from triple negative breast cancer patients , In Chinese Journal of Cancer, volume 34, 2015. [99] Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential clinical utility , In Oncotarget, volume 6, 2015. [98] Computational Cancer Biology: Education is a key to many locks , In BMC Cancer, volume 15, 2015. [97] Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data , In BMC Systems Biology, volume 9, 2015. [96] Graph Distance Mesures Based on Topological Indices Revisited , In Applied Mathematics and Computation, volume 266, 2015. [95] Structural Analysis of Treatment Cycles Representing Transitions Between Nursing Organizational Units Inferred from Diabetes , In PLoS ONE, volume 10, 2015. 2014 [94] Inference and validation of predictive gene networks from biomedical literature and gene expression data , In Genomics, volume 103, 2014. [93] NetBioV: An R package for visualizing large-scale data in Network Biology , In Bioinformatics, 2014. [92] Dry computational approaches for wet medical problems , In Journal of Translational Medicine, volume 12, 2014. [91] The gene regulatory network for breast cancer: Integrated regulatory landscape of cancer hallmarks , In Front. Genet., volume 5, 2014. [90] Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast , In Genomics Data, volume 2, 2014. [89] Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics , In Front. Genet., volume 5, 2014. [88] Probabilistic Inequalities for Evaluating Structural Network Measures , In Information Sciences, volume 288, 2014. [87] Untangling statistical and biological models to understand network inference: The need for a genomics network ontology , In Front. Genet., volume 5, 2014. [86] A Computational Approach to Construct a Multivariate Complete Graph Invariant , In Information Sciences, volume 260, 2014. [85] Interrelations of Graph Distance Measures Based on Topological Indices , In PLoS One, volume 9, 2014. [84] Entropy bounds for dendrimers , In Applied Mathematics and Computation, volume 242, 2014. [83] Enhancing our understanding of ways to analyze metagenomes , In Front. Genet., volume 5, 2014. [82] Gene regulatory networks and their applications: Understanding biological and medical problems in terms of networks , In Front. Cell Dev. Biol., volume 2, 2014. [81] Functional and genetic analysis of the colon cancer network , In BMC Bioinformatics, volume 15, 2014. [80] Relevance of different prior knowledge sources for inferring gene interaction networks , In Front. Genet., volume 5, 2014. [79] Comparative evaluation of gene set analysis approaches for RNA-Seq data , In BMC Bioinformatics, volume 15, 2014. [78] Netmes: Assessing gene network inference algorithms by ensemble network-based measures , In Evolutionary Bioinformatics, volume 10, 2014. [77] Gene Sets Net Correlations Analysis (GSNCA): A multivariate differential coexpression test for gene sets , In Bioinformatics, volume 30, 2014. 2013 [76] B-cell lymphoma gene regulatory networks: Biological consistency among inference methods , In Front. Genet., volume 4, 2013. [75] Enhancing systems medicine beyond genotype data by dynamic patient signatures: Having information and using it too , In Front. Genet., volume 4, 2013. [74] Learning Systems Biology: Conceptual Considerations Toward a Web-based Learning Platform , In Education Sciences, volume 3, 2013. [73] Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential , In Nucleic Acids Research, volume 6, 2013. [72] Personalized medicine: Has it started yet? A reconstruction of the early history , In Front Genet, volume 3, 2013. [71] Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: Environmental factors , In PeerJ, volume 1, 2013. [70] The human disease network: Opportunities for classification, diagnosis and prediction of disorders and disease genes , In Systems Biomedicine, volume 1, 2013. [69] Interfacing cellular networks of \textitS. cerevisiae and \textitE. coli: Connecting dynamic and genetic information , In BMC Genomics, volume 14, 2013. [68] [COMMODE] A Large-Scale Database of Molecular Descriptors using compounds from PubChem , In Source Code for Biology and Medicine, volume 8, 2013. [67] Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers , In PLoS ONE, volume 8, 2013. [66] Large-Scale Evaluation of Molecular Descriptors by Means of Clustering , In PLoS ONE, volume 8, 2013. [65] Structural properties and complexity of a new network class: Collatz step graphs , In PLoS ONE, volume 8, 2013. [64] An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants , In Advances in Computational Mathematics, volume 39, 2013. [63] Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data , In BMC Medicine, volume 11, 2013. [62] Network Nursing: Connections between Nursing and Complex Network Science , In International Journal of Nursing Knowledge, volume 24, 2013. 2012 [61] Assessment Method for a Power Analysis to Identify Differentially Expressed Pathways , In PLoS ONE, Public Library of Science, volume 7, 2012. [60] Statistical inference and reverse engineering of gene regulatory networks from observational expression data , In Frontiers in Genetics, volume 3, 2012. [59] Exploring statistical and population aspects of network complexity , In PLoS ONE, volume 7, 2012. [58] Limitations of the gene duplication model: Evolution of modules in protein interaction networks , In PLoS ONE, volume 7, 2012. [57] A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data , In Scientific Reports, volume 2, 2012. [56] Detecting sequence dependent transcriptional pauses from RNA and protein number time series , In BMC Bioinformatics, volume 13, 2012. [55] Harnessing the complexity of gene expression data from cancer: From single gene to structural pathway methods , In Biology Direct, volume 7, 2012. [54] An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants , In Advances in Computational Mathematics, 2012. [53] Bagging statistical network inference from large-scale gene expression data , In PLoS ONE, volume 7, 2012. [52] Standardisation of diagnostic biomarker concentrations in urine; the hematuria caveat , In PLoS ONE, volume 7, 2012. [51] Organizational structure of the peripheral gene regulatory network in B-cell lymphoma , In BMC Systems Biology, volume 6, 2012. [50] Universal construction mechanism for networks from one-dimensional symbol sequences , In Applied Mathematics and Computation, volume 219, 2012. [49] Evolutionary dynamics of the spatial Prisoner's Dilemma with self-inhibition , In Applied Mathematics and Computation, volume 218, 2012. [48] Gene set analysis for self-contained tests: complex null and specific alternative hypotheses , In Bioinformatics, volume 28, 2012. 2011 [47] Pathway analysis of expression data: deciphering functional building blocks of complex diseases , In PLoS Computational Biology, volume 7, 2011. [46] Influence of Statistical Estimators of Mutual Information and Data Heterogeneity on the Inference of Gene Regulatory Networks , In PLoS ONE, volume 6, 2011. [45] Structural Influence of gene networks on their inference: Analysis of C3NET , In Biology Direct, volume 6, 2011. [44] Structural Measures for Network Biology Using QuACN , In BMC Bioinformatics, volume 12, 2011. [43] Network Biology: A direct approach to study biological function , In Wiley Interdiscip Rev Syst Biol Med, volume 3, 2011. [42] Networks for Systems Biology: Conceptual Connection of Data and Function , In IET Systems Biology, volume 5, 2011. [41] Parametric construction of episode networks from pseudoperiodic time series based on mutual information , In PLoS ONE, volume 6, 2011. [40] Connections between Classical and Parametric Network Entropies , In PLoS ONE, volume 6, 2011. 2010 [39] Local network-based measures to assess the inferability of different regulatory networks , In IET Systems Biology, volume 4, 2010. [38] Statistic Complexity: Combining Kolmogorov Complexity with an Ensemble Approach , In PLoS ONE, volume 5, 2010. [37] Influence of the Time Scale on the Construction of Financial Networks , In PLoS ONE, volume 5, 2010. [36] Novel Information Measure for the Analysis of Chemical Graphs , In Bulletin of the Tomsk Polytechnic University, volume 316, 2010. [35] Identifying Critical Financial Networks of the DJIA: Towards a Network-based Index , In Complexity, volume 16, 2010. [34] Revealing differences in gene network inference algorithms on the network-level by ensemble methods , In Bioinformatics, volume 26, 2010. [33] Inferring the conservative causal core of gene regulatory networks , In BMC Systems Biology, volume 4, 2010. [32] Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility , In Physical Review E, volume 81, 2010. 2009 [31] Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets , In Bioinformatics, volume 25, 2009. [30] Predicting cell cycle regulated genes by causal interactions , In Plos One, volume 4, 2009. [29] Hierarchical coordination of periodic genes in the cell cycle of it Saccharomyces cerevisiae , In BMC Systems Biology, volume 3, 2009. [28] On Entropy-based Molecular Descriptors: Statistical Analysis of Real and Synthetic Chemical Structures , In Journal of Chemical Information and Modeling, volume 49, 2009. [27] Information Processing in the Transcriptional Regulatory Network of Yeast: Functional Robustness , In BMC Systems Biology, volume 3, 2009. [26] Fault Tolerance of Information Processing in Gene Networks , In Physica A: Statistical Mechanics and its Applications, volume 388, 2009. 2008 [25] The Structural Information Content of Chemical Networks , In Zeitschrift für Naturforschung A, volume 63a, 2008. [24] Entropy Bounds for Hierarchical Molecular Networks , In PLoS ONE, volume 3, 2008. [23] Robustness in Scale-free Networks: Comparing Directed and Undirected Networks , In International Journal of Modern Physics C, volume 19, 2008. [22] Structural Information Content of Networks: Graph Entropy based on Local Vertex Functionals , In Computational Biology and Chemistry, volume 32, 2008. [21] A Comparative Analysis of Multidimensional Features of Objects Resembling Sets of Graphs , In Applied Mathematics and Computation, volume 196, 2008. 2007 [20] Information Theoretic Measures of UHG Graphs with Low Computational Complexity , In Applied Mathematics and Computation, volume 190, 2007. [19] A Topological Algorithm for Identification of Structural Domains of Proteins , In BMC Bioinformatics, volume 8, 2007. () [18] Comparing Large Graphs Efficiently by Margines of Feature Vectors , In Applied Mathematics and Computation, volume 188, 2007. (Remark: Both authors contributed equally to this work.) [17] Topolocial Mappings between Graphs, Trees and Generalized Trees , In Applied Mathematics and Computation, volume 186, 2007. () [16] Nonlinear Time Series Prediction based on a Power-Law Noise Model , In International Journal of Modern Physics C, volume 18, 2007. [15] Harnessing naturally randomized transcription to infer regulatory relationships among genes , In Genome Biology, volume 8, 2007. [14] The Chronic Fatigue Syndrome: A Comparative Pathway Analysis , In Journal of Computational Biology, volume 14, 2007. [13] Structural Similarity of Directed Universal Hierarchical Graphs: A low Computational Complexity Approach , In Applied Mathematics and Computation, volume 194, 2007. 2006 [12] Perspectives of Graph Mining Techniques , In Rostocker Informatik Berichte, volume 30, 2006. [11] A Similarity Measure for Graphs with Low Computational Complexity , In Applied Mathematics and Computation, volume 182, 2006. () [10] Ranking Genes from DNA Microarray Data of Cervical Cancer by a local Tree Comparison , In International Journal of Biomedical Sciences, volume 1, 2006. [9] Algorithmic Computation of Knot Polynomials of Secondary Structure Elemtents of Proteins , In Journal of Computational Biology, volume 13, 2006. () [8] Influence of the neural network topology on the learning dynamics , In Neurocomputing, volume 69, 2006. () [7] Measuring the Structural Similarity of Web-based Documents: A novel Approach , In International Journal of Computational Intelligence, volume 3, 2006. () [6] A Heterosynaptic Learning Rule for Neural Networks , In International Journal of Modern Physics C, volume 17, 2006. 2005 [5] Stochastic Sznajd Model in Open Community , In International Journal of Modern Physics C, volume 16, 2005. [4] Active Learning in Recurrent Neural Networks Facilitated by an Hebb-like Learning Rule with Memory , In Neural Information Processing - Letters and Reviews, volume 9, 2005. [3] Self-organized annealing in laterally inhibited neural networks shows power law decay , In Neural Information Processing - Letters and Reviews, volume 7, 2005. 2001 [2] A constrained HMM-based approach to the estimation of perceptual switching dynamics in Pigeons , In Neurocomputing, volume 38-40, 2001. 2000 [1] Extracting the Dynamics of Perceptual Switching from Noisy Behaviour: An Application of Hidden Markov Modeling to Pecking Data from Pigeons , In Journal of Physiology (Paris), volume 94, 2000.

Journal Articles

2016, submitted | |

[118] | Can genome-scale gene regulatory networks be experimentally validated? Differences between biological and clinical validations , In , volume , 2016, submitted. |

[117] | Smoking and increased age in hematuria patients significantly confound the accuracy of classifiers for the diagnosis of urothelial cancer , In , volume , 2016, submitted. |

2016, revised | |

[116] | A Review of Connectivity Mapping and Computational Approaches in Pharmacogenomics , In Briefings in Bioinformatics, volume , 2016, revised. |

2016 | |

[115] | Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites , In Frontiers in Genetics, volume 7, 2016. |

[114] | Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules , In BMC Bioinformatics, volume 17, 2016. |

[113] | The Need for Formally Defining 'Modern Medicine' by Means of Experimental Design , In Frontiers in Genetics, volume 7, 2016. |

[112] | samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files , In Bioinformatics, volume , 2016. |

[111] | Fifty Years of Graph Matching, Network Alignment and Network Comparison , In Information Sciences, volume 346?347, 2016. |

[110] | The process of analyzing data is the emergent feature of data science , In Frontiers in Genetics, volume 7, 2016. |

[109] | A BRCA1 deficient, NF$\kappa$B driven immune signal predicts good outcome in Triple Negative breast cancer , In Oncotarget, volume 7, 2016. |

[108] | Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline , In Briefings in Bioinformatics, volume 17, 2016. |

2015, submitted | |

[107] | The evolution of modularity in protein networks: A second-order gene duplication model , In , 2015, submitted. |

2015 | |

[106] | Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices , In PLoS ONE, Public Library of Science, volume 10, 2015. |

[105] | Urinary Thrombomodulin Levels Were Significantly Higher Following Occupational Exposure to Chemicals, In The Presence of Dipstick Protein, But Not in the Presence of Dipstick Blood , In Biology and Medicine, volume 7, 2015. |

[104] | Graph distance measures based on topological indices revisited , In Applied Mathematics and Computation, volume 266, 2015. () |

[103] | Entropy of weighted graphs with Randi\'c weights , In Entropy, volume 17, 2015. |

[102] | Using shRNA experiments to validate gene regulatory networks , In Genomics Data, volume 4, 2015. () |

[101] | Biological networks: The microscope of the 21st century? , In Frontiers in Genetics, volume 6, 2015. |

[100] | Effects of subsampling on characteristics of RNA-seq data from triple negative breast cancer patients , In Chinese Journal of Cancer, volume 34, 2015. |

[99] | Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential clinical utility , In Oncotarget, volume 6, 2015. |

[98] | Computational Cancer Biology: Education is a key to many locks , In BMC Cancer, volume 15, 2015. |

[97] | Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data , In BMC Systems Biology, volume 9, 2015. |

[96] | Graph Distance Mesures Based on Topological Indices Revisited , In Applied Mathematics and Computation, volume 266, 2015. |

[95] | Structural Analysis of Treatment Cycles Representing Transitions Between Nursing Organizational Units Inferred from Diabetes , In PLoS ONE, volume 10, 2015. |

2014 | |

[94] | Inference and validation of predictive gene networks from biomedical literature and gene expression data , In Genomics, volume 103, 2014. |

[93] | NetBioV: An R package for visualizing large-scale data in Network Biology , In Bioinformatics, 2014. |

[92] | Dry computational approaches for wet medical problems , In Journal of Translational Medicine, volume 12, 2014. |

[91] | The gene regulatory network for breast cancer: Integrated regulatory landscape of cancer hallmarks , In Front. Genet., volume 5, 2014. |

[90] | Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast , In Genomics Data, volume 2, 2014. |

[89] | Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics , In Front. Genet., volume 5, 2014. |

[88] | Probabilistic Inequalities for Evaluating Structural Network Measures , In Information Sciences, volume 288, 2014. |

[87] | Untangling statistical and biological models to understand network inference: The need for a genomics network ontology , In Front. Genet., volume 5, 2014. |

[86] | A Computational Approach to Construct a Multivariate Complete Graph Invariant , In Information Sciences, volume 260, 2014. |

[85] | Interrelations of Graph Distance Measures Based on Topological Indices , In PLoS One, volume 9, 2014. |

[84] | Entropy bounds for dendrimers , In Applied Mathematics and Computation, volume 242, 2014. |

[83] | Enhancing our understanding of ways to analyze metagenomes , In Front. Genet., volume 5, 2014. |

[82] | Gene regulatory networks and their applications: Understanding biological and medical problems in terms of networks , In Front. Cell Dev. Biol., volume 2, 2014. |

[81] | Functional and genetic analysis of the colon cancer network , In BMC Bioinformatics, volume 15, 2014. |

[80] | Relevance of different prior knowledge sources for inferring gene interaction networks , In Front. Genet., volume 5, 2014. |

[79] | Comparative evaluation of gene set analysis approaches for RNA-Seq data , In BMC Bioinformatics, volume 15, 2014. |

[78] | Netmes: Assessing gene network inference algorithms by ensemble network-based measures , In Evolutionary Bioinformatics, volume 10, 2014. |

[77] | Gene Sets Net Correlations Analysis (GSNCA): A multivariate differential coexpression test for gene sets , In Bioinformatics, volume 30, 2014. |

2013 | |

[76] | B-cell lymphoma gene regulatory networks: Biological consistency among inference methods , In Front. Genet., volume 4, 2013. |

[75] | Enhancing systems medicine beyond genotype data by dynamic patient signatures: Having information and using it too , In Front. Genet., volume 4, 2013. |

[74] | Learning Systems Biology: Conceptual Considerations Toward a Web-based Learning Platform , In Education Sciences, volume 3, 2013. |

[73] | Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential , In Nucleic Acids Research, volume 6, 2013. |

[72] | Personalized medicine: Has it started yet? A reconstruction of the early history , In Front Genet, volume 3, 2013. |

[71] | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: Environmental factors , In PeerJ, volume 1, 2013. |

[70] | The human disease network: Opportunities for classification, diagnosis and prediction of disorders and disease genes , In Systems Biomedicine, volume 1, 2013. |

[69] | Interfacing cellular networks of \textitS. cerevisiae and \textitE. coli: Connecting dynamic and genetic information , In BMC Genomics, volume 14, 2013. |

[68] | [COMMODE] A Large-Scale Database of Molecular Descriptors using compounds from PubChem , In Source Code for Biology and Medicine, volume 8, 2013. |

[67] | Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers , In PLoS ONE, volume 8, 2013. |

[66] | Large-Scale Evaluation of Molecular Descriptors by Means of Clustering , In PLoS ONE, volume 8, 2013. |

[65] | Structural properties and complexity of a new network class: Collatz step graphs , In PLoS ONE, volume 8, 2013. |

[64] | An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants , In Advances in Computational Mathematics, volume 39, 2013. |

[63] | Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data , In BMC Medicine, volume 11, 2013. |

[62] | Network Nursing: Connections between Nursing and Complex Network Science , In International Journal of Nursing Knowledge, volume 24, 2013. |

2012 | |

[61] | Assessment Method for a Power Analysis to Identify Differentially Expressed Pathways , In PLoS ONE, Public Library of Science, volume 7, 2012. |

[60] | Statistical inference and reverse engineering of gene regulatory networks from observational expression data , In Frontiers in Genetics, volume 3, 2012. |

[59] | Exploring statistical and population aspects of network complexity , In PLoS ONE, volume 7, 2012. |

[58] | Limitations of the gene duplication model: Evolution of modules in protein interaction networks , In PLoS ONE, volume 7, 2012. |

[57] | A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data , In Scientific Reports, volume 2, 2012. |

[56] | Detecting sequence dependent transcriptional pauses from RNA and protein number time series , In BMC Bioinformatics, volume 13, 2012. |

[55] | Harnessing the complexity of gene expression data from cancer: From single gene to structural pathway methods , In Biology Direct, volume 7, 2012. |

[54] | An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants , In Advances in Computational Mathematics, 2012. |

[53] | Bagging statistical network inference from large-scale gene expression data , In PLoS ONE, volume 7, 2012. |

[52] | Standardisation of diagnostic biomarker concentrations in urine; the hematuria caveat , In PLoS ONE, volume 7, 2012. |

[51] | Organizational structure of the peripheral gene regulatory network in B-cell lymphoma , In BMC Systems Biology, volume 6, 2012. |

[50] | Universal construction mechanism for networks from one-dimensional symbol sequences , In Applied Mathematics and Computation, volume 219, 2012. |

[49] | Evolutionary dynamics of the spatial Prisoner's Dilemma with self-inhibition , In Applied Mathematics and Computation, volume 218, 2012. |

[48] | Gene set analysis for self-contained tests: complex null and specific alternative hypotheses , In Bioinformatics, volume 28, 2012. |

2011 | |

[47] | Pathway analysis of expression data: deciphering functional building blocks of complex diseases , In PLoS Computational Biology, volume 7, 2011. |

[46] | Influence of Statistical Estimators of Mutual Information and Data Heterogeneity on the Inference of Gene Regulatory Networks , In PLoS ONE, volume 6, 2011. |

[45] | Structural Influence of gene networks on their inference: Analysis of C3NET , In Biology Direct, volume 6, 2011. |

[44] | Structural Measures for Network Biology Using QuACN , In BMC Bioinformatics, volume 12, 2011. |

[43] | Network Biology: A direct approach to study biological function , In Wiley Interdiscip Rev Syst Biol Med, volume 3, 2011. |

[42] | Networks for Systems Biology: Conceptual Connection of Data and Function , In IET Systems Biology, volume 5, 2011. |

[41] | Parametric construction of episode networks from pseudoperiodic time series based on mutual information , In PLoS ONE, volume 6, 2011. |

[40] | Connections between Classical and Parametric Network Entropies , In PLoS ONE, volume 6, 2011. |

2010 | |

[39] | Local network-based measures to assess the inferability of different regulatory networks , In IET Systems Biology, volume 4, 2010. |

[38] | Statistic Complexity: Combining Kolmogorov Complexity with an Ensemble Approach , In PLoS ONE, volume 5, 2010. |

[37] | Influence of the Time Scale on the Construction of Financial Networks , In PLoS ONE, volume 5, 2010. |

[36] | Novel Information Measure for the Analysis of Chemical Graphs , In Bulletin of the Tomsk Polytechnic University, volume 316, 2010. |

[35] | Identifying Critical Financial Networks of the DJIA: Towards a Network-based Index , In Complexity, volume 16, 2010. |

[34] | Revealing differences in gene network inference algorithms on the network-level by ensemble methods , In Bioinformatics, volume 26, 2010. |

[33] | Inferring the conservative causal core of gene regulatory networks , In BMC Systems Biology, volume 4, 2010. |

[32] | Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility , In Physical Review E, volume 81, 2010. |

2009 | |

[31] | Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets , In Bioinformatics, volume 25, 2009. |

[30] | Predicting cell cycle regulated genes by causal interactions , In Plos One, volume 4, 2009. |

[29] | Hierarchical coordination of periodic genes in the cell cycle of it Saccharomyces cerevisiae , In BMC Systems Biology, volume 3, 2009. |

[28] | On Entropy-based Molecular Descriptors: Statistical Analysis of Real and Synthetic Chemical Structures , In Journal of Chemical Information and Modeling, volume 49, 2009. |

[27] | Information Processing in the Transcriptional Regulatory Network of Yeast: Functional Robustness , In BMC Systems Biology, volume 3, 2009. |

[26] | Fault Tolerance of Information Processing in Gene Networks , In Physica A: Statistical Mechanics and its Applications, volume 388, 2009. |

2008 | |

[25] | The Structural Information Content of Chemical Networks , In Zeitschrift für Naturforschung A, volume 63a, 2008. |

[24] | Entropy Bounds for Hierarchical Molecular Networks , In PLoS ONE, volume 3, 2008. |

[23] | Robustness in Scale-free Networks: Comparing Directed and Undirected Networks , In International Journal of Modern Physics C, volume 19, 2008. |

[22] | Structural Information Content of Networks: Graph Entropy based on Local Vertex Functionals , In Computational Biology and Chemistry, volume 32, 2008. |

[21] | A Comparative Analysis of Multidimensional Features of Objects Resembling Sets of Graphs , In Applied Mathematics and Computation, volume 196, 2008. |

2007 | |

[20] | Information Theoretic Measures of UHG Graphs with Low Computational Complexity , In Applied Mathematics and Computation, volume 190, 2007. |

[19] | A Topological Algorithm for Identification of Structural Domains of Proteins , In BMC Bioinformatics, volume 8, 2007. () |

[18] | Comparing Large Graphs Efficiently by Margines of Feature Vectors , In Applied Mathematics and Computation, volume 188, 2007. (Remark: Both authors contributed equally to this work.) |

[17] | Topolocial Mappings between Graphs, Trees and Generalized Trees , In Applied Mathematics and Computation, volume 186, 2007. () |

[16] | Nonlinear Time Series Prediction based on a Power-Law Noise Model , In International Journal of Modern Physics C, volume 18, 2007. |

[15] | Harnessing naturally randomized transcription to infer regulatory relationships among genes , In Genome Biology, volume 8, 2007. |

[14] | The Chronic Fatigue Syndrome: A Comparative Pathway Analysis , In Journal of Computational Biology, volume 14, 2007. |

[13] | Structural Similarity of Directed Universal Hierarchical Graphs: A low Computational Complexity Approach , In Applied Mathematics and Computation, volume 194, 2007. |

2006 | |

[12] | Perspectives of Graph Mining Techniques , In Rostocker Informatik Berichte, volume 30, 2006. |

[11] | A Similarity Measure for Graphs with Low Computational Complexity , In Applied Mathematics and Computation, volume 182, 2006. () |

[10] | Ranking Genes from DNA Microarray Data of Cervical Cancer by a local Tree Comparison , In International Journal of Biomedical Sciences, volume 1, 2006. |

[9] | Algorithmic Computation of Knot Polynomials of Secondary Structure Elemtents of Proteins , In Journal of Computational Biology, volume 13, 2006. () |

[8] | Influence of the neural network topology on the learning dynamics , In Neurocomputing, volume 69, 2006. () |

[7] | Measuring the Structural Similarity of Web-based Documents: A novel Approach , In International Journal of Computational Intelligence, volume 3, 2006. () |

[6] | A Heterosynaptic Learning Rule for Neural Networks , In International Journal of Modern Physics C, volume 17, 2006. |

2005 | |

[5] | Stochastic Sznajd Model in Open Community , In International Journal of Modern Physics C, volume 16, 2005. |

[4] | Active Learning in Recurrent Neural Networks Facilitated by an Hebb-like Learning Rule with Memory , In Neural Information Processing - Letters and Reviews, volume 9, 2005. |

[3] | Self-organized annealing in laterally inhibited neural networks shows power law decay , In Neural Information Processing - Letters and Reviews, volume 7, 2005. |

2001 | |

[2] | A constrained HMM-based approach to the estimation of perceptual switching dynamics in Pigeons , In Neurocomputing, volume 38-40, 2001. |

2000 | |

[1] | Extracting the Dynamics of Perceptual Switching from Noisy Behaviour: An Application of Hidden Markov Modeling to Pecking Data from Pigeons , In Journal of Physiology (Paris), volume 94, 2000. |