Danail Bonchev

Virginia Commonwealth University | VCU · Center for the Study of Biological Complexity

Welcome From Chairs Dear colleagues worldwide, we are glad to invite you to MOL2NET-05, International Conference on Multidisciplinary Sciences, ISSN: 2624-5078, MDPI SciForum, Basel, Switzerland, 2019. MOL2NET is a year-round conference series with multiple associated workshops worldwide running and open to submissions almost all the year, please r...

Conference: Proceedings of the conference MOL2NET International Conference on Multidisciplinary Sciences (4th edition), 2018 is part of a year-round worldwide conference series hosted by MDPI Sciforum, Basel, Switzerland. This conference series has had organized more than 20 associated workshop series in universities worldwide: USA, France, Portuga...

Objective: The healing of wounds is critical in protecting the human body against environmental factors. The mechanisms involving protein expression during this complex physiological process have not been fully elucidated. Approach: Here, we use reverse-phase protein microarrays (RPPA) involving 94 phosphoproteins to study tissue samples from tu...

We are glad to invite all colleagues worldwide to participate on a new edition of this International Conference Series. The official title of this conference series is MOL2NET International Conference Series on Multidisciplinary Sciences. MOL2NET (the conference running title) is the acronym of the lemma of the conference: From Molecules to Network...

Proceedings of the conference MOL2NET International Conference on Multidisciplinary Sciences (3rd edition), 2017. Year-Round conference series hosted by MDPI Sciforum, Basel, Switzerland. These conferences have more than 10 associated workshop series in universities of USA, Spain, China, Chile, Brazil, etc. These workshop series run in person and/o...

Proceedings of MOL2NET International Conference on Multidisciplinary Sciences (2nd edition), 2016. Year-Round conferences series hosted by MDPI Sciforum, Basel, Switzerland with > 10 associated in person workshops in USA, Spain, China, Chile, Brazil, etc. Some of the workshops are SRI-08 St Thomas University (STU)- Miami Dade College (MDC), Miami,...

CONFERENCE SERIES CALL FOR PAPERS ‪We are glad to invite all colleagues worldwide to participate on the MOL2NET International Conference Series on Multidisciplinary Sciences. MOL2NET (the conference running title) is the acronym of the lemma of the conference: From Molecules to Networks. This running title is inspired by the possibility of multidis...

Four-set Venn diagram of the overlap of significantly differentially expressed genes (SDEGs).

Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Usi...

Network-based approaches are powerful and beneficial tools to study complex systems in their entirety, elucidating the essential factors that turn the multitude of individual elements into a functional system. In this study we used critical network topology descriptors and guilt-by-association rule to explore and understand the significant molecula...

Biological processes and genes implicated in the Alzheimer’s disease. Courtesy: Alzheimer’s disease pathway from KEGG database, retrieved on Apr 3, 2013. Publicly available at http://www.genome.jp/kegg-bin/show_pathway?hsa05010. (TIF)

List of 214 significantly differentially expressed genes (SDEGs). (XLSX)

In this study we offer an approach to network physiology, which proceeds from transcriptomic data and uses gene ontology analysis to identify the biological processes most enriched in several critical time points of wound healing process (days 0, 3 and 7). The top-ranking differentially expressed genes for each process were used to build two networ...

In this eBook we introduce our readers to one of the most comprehensive and thematically diverse treatise on the emerging discipline of mathematical chemistry, or, more accurately, discrete mathematical chemistry. Although mathematical representation and characterization of chemical objects were known for a long time, the incursion of discrete math...

The study offers approaches to several unresolved questions of network motifs un-ambiguous identification and classification, and presents an online resource which will help disambiguate future discussions. A canonical identification number is introduced for each motif. A taxonomy of unidirectional motifs is proposed based on motifs nodes distribut...

A procedure was developed, on the basis of the distance matrix of the graph, for the calculation of the specific π-electron energy and energy gap in polymerhomologous series and infinite polymers. 25 conjugated polymers were examined by this procedure and a fairly good correlation between these energy characteristics and the sum of all distances in...

This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical...

Graph theory based descriptors of molecular structure play important role in QSPR/ QSAR models. This chapter reviews some attempts to optimize the characterization of molecular structure via an integrated representation that accounts in a systemic manner for the contributions of all substructures. In its simplest version this approach counts the su...

The wound healing process is well-understood on the cellular and tissue level; however, its complex molecular mechanisms are not yet uncovered in their entirety. Viewing wounds as perturbed molecular networks provides the tools for analyzing and optimizing the healing process. It helps to answer specific questions that lead to better understanding...

Network-based systems biology tools including Pathway Studio 9.0 were used to identify Parkinson's disease (PD) critical molecular players, drug targets, and underlying biological processes. Utilizing several microarray gene expression datasets, biomolecular networks such as direct interaction, shortest path, and microRNA regulatory networks were c...

Network-based systems biology tools including Pathway Studio 9.0 were used to identify Parkinson’s disease (PD) critical molecular players, drug targets, and underlying biological processes. Utilizing several microarray gene expression datasets, biomolecular networks such as direct interaction, shortest path, and microRNA regulatory networks were c...

This handbook and ready reference presents a combination of statistical, information-theoretic, and data analysis methods to meet the challenge of designing empirical models involving molecular descriptors within bioinformatics. The topics range from investigating information processing in chemical and biological networks to studying statistical an...

This study is a part of a project investigating the molecular determinants of neurological diseases. To account for the systemic nature of these diseases we proceeded from a well established list of 38 schizophrenia-related genes (Allen et al., 2008; Ross et al., 2006) and investigated their closest network environment. The created networks were co...

A clear perception of gene essentiality in bacterial pathogens is pivotal for identifying drug targets to combat emergence of new pathogens and antibiotic-resistant bacteria, for synthetic biology, and for understanding the origins of life. We have constructed a comprehensive set of deletion mutants and systematically identified a clearly defined s...

Supplementary Figures

Supplementary Tables

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

We introduce several series of novel ZE-isomerism descriptors derived directly from two-dimensional molecular topology. These descriptors make use of a quantity named ZE-isomerism correction, which is added to the vertex degrees of atoms connected by double bonds in Z and E configurations. This approach is similar to the one described previously fo...

The powerful OASIS (optimized approach based on structural indices set) approach is applied to the anticancer activity of a series of vitamin A analogs. The best three- and four-variable models obtained via the OASIS technique have correlation coefficients of 0.973 vs. 0.990 and standard deviations s2 = 0.11 and 0.05, respectively. The models incor...

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Software for network motifs and modules is briefly reviewed, along with programs for network comparison. The three major software packages for network analysis, CYTOSCAPE, INGENUITY and PATHWAY STUDIO, and their associated databases, are compared in detail. A comparative test evaluated how these software packages perform the search for key terms an...

Comparison of metabolic networks across species is a key to understanding how evolutionary pressures shape these networks. By selecting taxa representative of different lineages or lifestyles and using a comprehensive set of descriptors of the structure and complexity of their metabolic networks, one can highlight both qualitative and quantitative...

Values of the NIP descriptors. The average value and standard deviation of all 52 NIP descriptors is calculated for all taxa of each group considered in the study. Those NIP descriptors revealed as the best discriminative for a given taxa groups comparison are highlighted in bold. P-values are obtained from Kruskal-Wallis one-way analysis of varian...

Network descriptors. Topological and information-theoretic network descriptors used in this study.

Effects of lineage and environment on pathways frequency, connectivity and centrality. The variation of six scores of frequency, connectivity and centrality, and the p-value evaluating the significance of this variation (calculated by either a Fisher's exact or Mann-Whitney U-test) are reported for each metabolic pathway. P-values are corrected for...

Classification models. List of the classification models with the best performance in discriminating taxa groups based on NIP descriptor values.

Groups of taxa. List of the 743 taxa considered in this study, sorted per group of common lineage, environment or life-style, together with the corresponding KEGG identifiers.

Training sets. NIP descriptor values and group membership of the 743 taxa considered in this study.

Two strategies for fighting cancer by modulating FASL-induced apoptosis were modeled by 2D-cellular automata. Our models predict that cancer cells can be killed by maximizing the apoptosis via joint suppression of FLIP and IAP inhibitors by siRNA and SMAC proteins, respectively. It was also predicted that the presumed feedback loop CASP3-->CASP9-->...

A preceding study analysed how the topology of network motifs affects the overall rate of the underlying biochemical processes. Surprisingly, it was shown that topologically non-isomorphic motifs can still be isodynamic in the sense that they exhibit the exact same performance rate. Because of the high prevalence of feed-forward functional modules...

The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques...

The complex interactions that characterize acute wound healing have stymied the development of effective therapeutic modalities. The use of computational models holds the promise to improve our basic approach to understanding the process. By modifying an existing ordinary differential equation model of systemic inflammation to simulate local wound...

A series of three descriptors of network complexity is introduced by combining the vertex degree distribution with that of vertex distance. The new small-world connectivity descriptors (termed also Bourgas indices, B1-B3) mirror the increase in network complexity with increasing vertex degrees and/or with decreasing network radius (the "small-world...

A topological index, based on the distance matrix of a molecule and derived by means of information theory, is proposed for characterization of skeletal branching. In all cases studied it has differentiated isomeric structures. The proposed index has been used rather satisfactorily for predicting the chromatographic retention indices of alkylbenzen...

Information is a concept of no less importance than matter or energy. Information has been described as a measure of the variety in a given system. We review several of the indices of molecular information, including those indices related to molecular composition, molecular symmetry, graph automorphism, graph coloring, and connectivity as measured...

A series of three descriptors of network complexity is introduced by combining the vertex degree distribution with that of vertex distance. The new small-world connectivity descriptors (termed also Bourgas indices, B1-B3) mirror the increase in network complexity with increasing vertex degrees and/or with decreasing network radius (the "small-world...

Trace evidences of natural history are preserved, not only in the sequences of genes and proteins, but also in the functional wiring of biological networks. To date, phylogenetic inference has been recovered from data involving intrinsic topological properties of enzymatic and pathway networks. These findings demonstrate that network structure is no...

Enrichment of longevity-associated genes in the Composite shortest-path longevity network. (0.08 MB PDF)

Relation table for the composite shortest path longevity network. (0.16 MB PDF)

Replicative life span analysis of single-gene deletion strains corresponding to genes in the binding shortest-path longevity network. (0.14 MB PDF)

Replicative life span analysis of 564 randomly selected single-gene deletion strains. (0.36 MB PDF)

The first neighbors longevity network has less predictive power than the Binding SPLN. (0.17 MB PDF)

Distribution of mean replicative life spans for 5 and 10 cell sets of BY4742 mother cells. (0.13 MB PDF)

Set of yeast genes reported to be associated with increased replicative life span used to construct the shortest-path longevity network. (0.11 MB PDF)

Genes contained in both the randomly selected set of 564 single-gene deletion strains and the predicted longevity associated genes in the binding shortest path longevity network. (0.12 MB PDF)

Deletion of YPT6, a component of the composite shortest-path longevity network, increases replicative life span. (0.11 MB PDF)

Components of the Binding shortest-path longevity network. (0.10 MB PDF)

Although metabolic reactions are unquestionably shaped by evolutionary processes, the degree to which the overall structure and complexity of their interconnections are linked to the phylogeny of species has not been evaluated in depth. Here, we apply an original metabolome representation, termed Network of Interacting Pathways or NIP, with a combi...